Over the last decades, greenhouse gas (GHG) emissions have grown at an increasing rate, which is likely to continue on the long-term trend. These emissions must be significantly reduced to avoid the worst impacts of climate change. As the world becomes more urbanized, cities stand at the forefront of efforts to achieve this goal. GHG emissions flow in and out of the administrative and geographical limits of a city, and interdisciplinary information is needed to pursue low-emission urban development strategies. Existing GHG inventory tools and procedures favor scaled-down estimations and direct emission sources. Policy makers cannot rely on scaled-down data from national GHG inventories to take action on a neighborhood level. As the geographic coverage of a GHG inventory gets smaller, emission activities that occur within the defined boundaries are intrinsically interconnected with ‘out-of-bound’ areas. In this case, accounting for emissions occurring outside a neighborhood is not an option, but a requirement. This paper presents a comparison among existing GHG emissions tools and methodologies, focusing on the problems that arise when using top-down Emissions factors to calculate indirect emissions.